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The Gulf of Alaska is a highly productive ecosystem that supports fisheries and subsistence harvesting of marine resources. The highly productive summer season begins with a bloom that is dominated by diatoms. Both river and submarine groundwater discharge have been recognized as substantial terrestrial nutrient (nitrate and silicate) sources to the Gulf’s coastal waters. Here, the response of in-situ phytoplankton to groundwater and river water additions was evaluated via a bioassay incubation experiment. Special attention was given to diatom genera, as previous studies have shown that submarine groundwater discharge preferentially induces growth of diatoms. The abundance of Pseudo-nitzschia spp., Chaetoceros spp., and Leptocylindrus spp. increased significantly in groundwater and river water containing treatments. Although groundwater and river water are both rich in nitrate and silicate, groundwater treatments with a higher salinity favored a higher relative abundance of Pseudo-nitzschia spp. Conversely, in the highest river water concentration treatments with lower salinity, relative abundances of Pseudo-nitzschia spp. decreased, while Chaetoceros spp. and Leptocylindrus spp. increased. Total abundances of all three genera increased in the lower salinity treatments. These findings could portend changes in the phytoplankton community composition in the Gulf of Alaska as the climate warms and river discharge increases in the coming decades. Furthermore, the findings support previous assertions that submarine groundwater discharge, with higher salinity than river water, is a preferable source of nutrients to the genus Pseudo-nitzschia.